Project Summary Premature birth is the main cause of infant morbidity and mortality worldwide. While recent research suggests that a diverse vaginal microbiota is linked to premature delivery, no firm associations with pregnancy and preterm birth have been proven. Similarly, although it is known that gut microorganisms play key roles in human function, and that pregnancy is regarded as a special immune state, no correlations with preterm delivery have been clearly established. This project involves a longitudinal study of gene and genome compositions, and their expression profiles, of both the vaginal and gut mucosa and their microbiome during pregnancy to determine their potential contributions to host physiology and premature birth. The goals of this proposal are to identify the vaginal and gut community structures during pregnancy to determine genome-level patterns associated with preterm birth; to reveal microbial gene activity early in pregnancy that predicts preterm birth; and to determine the impact of the microbiome on host physiology during pregnancy. These goals will be addressed by pursuing the following specific aims: 1) Characterize the metagenomes of vaginal and gut microbial communities, and their associated metabolic pathways in term and preterm pregnancies; 2) Define gene expression profiles of the vaginal and gut microbial communities in term and preterm pregnancies; and 3) Determine human gene expression profiles in term and preterm pregnancies and correlate them with vaginal and gut microbiome gene expression profiles. A cohort of 40 pregnant subjects who have collected monthly vaginal and stool samples throughout pregnancy will be selected. High-throughput DNA and RNA sequencing will be used to recover complete and partial genomes of vaginal and gut microbial organisms, and their gene expression profiles over time, and statistical associations with human gene expression and preterm birth will be determined. The significance of the study lays in its innovative approach and design: seeking to understand the relationships of the human microbiome with the progression of pregnancy and with the associated host physiology using state- of-the-art sequencing approaches and statistical methods. This work may lead to better predictors and new interventions of women at risk for preterm labor. It will also set the groundwork for future studies of the human microbiome and its role in human physiology, health and disease.